Recent molecular studies have suggested that the basal parasitic flatworms (Neodermata) had a simple life cycle, while more derived parasitic flatworms (Cestoda, Trematoda) developed complex life cycles. The intermediate stages of cestodes and trematodes have commonly been implicated in the formation of pearls or other shell secretions in recent bivalves. Late Paleozoic blister and early Mesozoic free pearls in fossil bivalves and other mollusks have therefore often been used as an indication for the presence of complex parasite life cycles. We investigated the occurrence of fossil pearls in mollusks as well parasitic flatworms fossils through geological time in an up to date ecological and phylogenetic framework. Their fossil record proves to be extremely biased, particularly within the Paleozoic and Mesozoic. Furthermore, the occurrence of pearls in distantly related orders as well as various other mollusk phyla suggests an ancient origin of pearl-like structures in the earliest shelled mollusks. Although the flatworm body fossil record is very poor, it does agree with the idea that parasitic flatworms coevolved with their vertebrate hosts to some extent. In absence of reliable parasitic flatworm fossils, the host fossil record is often used to calibrate molecular clocks. Using the host fossil record to test the hypothesis of coevolution leads to circularity, which might be resolved by calibrating parasite molecular clocks with biogeographic events instead.

Establishing an evolutionary timescale is the fundamental yet elusive goal of the earth and life sciences. Molecular clock methodology has usurped completely the role of the incomplete fossil record in establishing an evolutionary timescale but, ironically, it remains reliant on palaeontological data for calibration. Not surprisingly, it has become popular to eschew the fossil evidence entirely, instead calibrating divergence time analyses using geochronologically dated tectonic events that have left a phylogenetic footprint of divergence in evolutionary lineages. Unfortunately, tectonic calibrations have not enjoyed the same scrutiny and, therefore the development, as fossil calibrations. The profound accuracy and precision of geochronological dates of rock units belies their accuracy and precision in dating divergence events because: these biogeographic calibrations are rarely, if ever, justified; (ii) in eschewing fossil evidence, biogeographic calibrations assume the biogeography of living organisms is a faithful reflection of their ancestral lineages; (iii) age evidence is equally rarely established; (iv) tectonic episodes are protracted and so they should be represented by spans of time, not single dates; (v) biogeographic events have a different impact on lineages dependent on their ecology. These limitations can be overcome or, at least controlled for since, like fossil calibrations, vicariance-based calibrations can be implemented as probabilistic constraints that span an interval of time, entertaining the probability that the tectonic event was causal to the calibrating node, (ii) errors in the accuracy of dating the tectonic event, (iii) the temporal extent of the tectonic episode, (iv) the differential impact of the tectonic event on organisms with different ecologies. Finally, we would argue that palaeontological evidence can add to knowledge of the historical biogeography and ecology of evolutionary lineages supplementing insights provided by the extant biodiversity.